GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Sinorhizobium meliloti 1021

Align Metal-independent phosphoserine phosphatase; iPSP; Phosphoglycerate mutase-like protein 3; EC 3.1.3.3 (characterized)
to candidate SMc00006 SMc00006 hypothetical protein

Query= SwissProt::F4KI56
         (238 letters)



>FitnessBrowser__Smeli:SMc00006
          Length = 194

 Score = 62.8 bits (151), Expect = 5e-15
 Identities = 51/165 (30%), Positives = 78/165 (47%), Gaps = 12/165 (7%)

Query: 27  IVLVRHGETTWNAAGRIQGQIESDLNEVGLKQA----VAIAERLGKEERPVAVYSSDLKR 82
           I +VRHG+T WNA  R+QGQ +  LNE G +QA    VA++  +G         SS L R
Sbjct: 3   IYMVRHGQTDWNAESRLQGQKDIPLNETGRQQATGNGVALSRIIGSGAADFDFVSSPLGR 62

Query: 83  AKDTALMIAKTCFCPEVIEVPD--LKERHVGSLQGLYWKEGAEKEPEAYSAFFSSQNDLE 140
            ++T   + +      +    D  LKE   G  +G    E     PE  +    ++ D  
Sbjct: 63  TRETMERLRRAMDLDPLAYRTDERLKEVSFGDWEGYTLPELKRLVPERIAERRVAKWDFI 122

Query: 141 IPG-GGESFDQLADRSMDALEQIAKKHKGERVIVVTHGGVLRAIY 184
            PG   ES++ L+ R    L  + +       + V+HGGV+RA++
Sbjct: 123 PPGPDAESYEILSWRVGAWLRSVTRP-----TVCVSHGGVIRALF 162


Lambda     K      H
   0.315    0.132    0.387 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 141
Number of extensions: 10
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 238
Length of database: 194
Length adjustment: 22
Effective length of query: 216
Effective length of database: 172
Effective search space:    37152
Effective search space used:    37152
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory